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Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http:\/\/moodle.fct.unl.pt\/course\/view.php?id=2079 or https:\/\/sourceforge.net\/projects\/bidiblast\/ under the GNU GPL license.<\/jats:p>","DOI":"10.1016\/s1672-0229(10)60015-0","type":"journal-article","created":{"date-parts":[[2010,8,5]],"date-time":"2010-08-05T09:10:46Z","timestamp":1280999446000},"page":"135-138","source":"Crossref","is-referenced-by-count":1,"title":["BiDiBlast: Comparative Genomics Pipeline for the PC"],"prefix":"10.1093","volume":"8","author":[{"given":"Jo\u00e3o M.G.C.F.","family":"de Almeida","sequence":"first","affiliation":[{"name":"Centro de Recursos Microbiol\u00f3gicos (CREM), Departamento de Ci\u00eancias da Vida, Faculdade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa , Caparica, Quinta da Torre, 2829-516 , Portugal"}]}],"member":"286","published-online":{"date-parts":[[2010,8,4]]},"reference":[{"key":"2024051008271862800_bib1","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/nar\/28.1.45","article-title":"The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000","volume":"28","author":"Bairoch","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2024051008271862800_bib2","doi-asserted-by":"crossref","first-page":"6239","DOI":"10.1073\/pnas.95.11.6239","article-title":"Genomic evidence for two functionally distinct gene classes","volume":"95","author":"Rivera","year":"1998","journal-title":"Proc. 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